Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 02:39:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/04_2023/6x19_21993_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/04_2023/6x19_21993.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/04_2023/6x19_21993_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/04_2023/6x19_21993_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/04_2023/6x19_21993_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/04_2023/6x19_21993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/04_2023/6x19_21993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/04_2023/6x19_21993_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x19_21993/04_2023/6x19_21993_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 843 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 62 5.16 5 C 6462 2.51 5 N 1748 2.21 5 O 2003 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R GLU 76": "OE1" <-> "OE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 10277 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2876 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3268 Unusual residues: {'UK1': 1} Classifications: {'peptide': 387, 'undetermined': 1} Link IDs: {'PTRANS': 14, 'TRANS': 372, None: 1} Not linked: pdbres="GLU R 423 " pdbres="UK1 R 501 " Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 30 Classifications: {'water': 30} Link IDs: {None: 29} Time building chain proxies: 5.44, per 1000 atoms: 0.53 Number of scatterers: 10277 At special positions: 0 Unit cell: (115.37, 96.28, 170.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 F 2 9.00 O 2003 8.00 N 1748 7.00 C 6462 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.01 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.05 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.44 Conformation dependent library (CDL) restraints added in 1.5 seconds 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 11 sheets defined 41.3% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.990A pdb=" N GLN A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 109 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 157 through 165 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.848A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.728A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.548A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'N' and resid 109 through 111 No H-bonds generated for 'chain 'N' and resid 109 through 111' Processing helix chain 'R' and resid 32 through 52 removed outlier: 4.029A pdb=" N GLN R 37 " --> pdb=" O TRP R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 116 No H-bonds generated for 'chain 'R' and resid 114 through 116' Processing helix chain 'R' and resid 124 through 126 No H-bonds generated for 'chain 'R' and resid 124 through 126' Processing helix chain 'R' and resid 137 through 140 No H-bonds generated for 'chain 'R' and resid 137 through 140' Processing helix chain 'R' and resid 142 through 166 Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing helix chain 'R' and resid 175 through 207 Processing helix chain 'R' and resid 211 through 222 removed outlier: 5.074A pdb=" N ASP R 215 " --> pdb=" O HIS R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 256 Processing helix chain 'R' and resid 262 through 274 removed outlier: 3.698A pdb=" N PHE R 266 " --> pdb=" O GLU R 262 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 291 removed outlier: 3.686A pdb=" N VAL R 281 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL R 282 " --> pdb=" O LEU R 279 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 3.504A pdb=" N VAL R 287 " --> pdb=" O TRP R 284 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR R 291 " --> pdb=" O LYS R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 337 removed outlier: 5.282A pdb=" N LEU R 311 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.602A pdb=" N PHE R 315 " --> pdb=" O PRO R 312 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL R 319 " --> pdb=" O ALA R 316 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 322 " --> pdb=" O VAL R 319 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL R 327 " --> pdb=" O PHE R 324 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS R 329 " --> pdb=" O ARG R 326 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS R 336 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 369 Processing helix chain 'R' and resid 379 through 392 removed outlier: 3.691A pdb=" N LYS R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 402 Processing helix chain 'R' and resid 407 through 422 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.099A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.892A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.764A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.555A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.738A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.605A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.439A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.562A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 93 through 98 removed outlier: 5.970A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 80 through 83 451 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1661 1.32 - 1.44: 2925 1.44 - 1.57: 5697 1.57 - 1.69: 11 1.69 - 1.82: 85 Bond restraints: 10379 Sorted by residual: bond pdb=" C03 UK1 R 501 " pdb=" N07 UK1 R 501 " ideal model delta sigma weight residual 1.478 1.722 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C46 UK1 R 501 " pdb=" C51 UK1 R 501 " ideal model delta sigma weight residual 1.390 1.546 -0.156 2.00e-02 2.50e+03 6.06e+01 bond pdb=" C28 UK1 R 501 " pdb=" C60 UK1 R 501 " ideal model delta sigma weight residual 1.524 1.674 -0.150 2.00e-02 2.50e+03 5.61e+01 bond pdb=" C46 UK1 R 501 " pdb=" N43 UK1 R 501 " ideal model delta sigma weight residual 1.481 1.628 -0.147 2.00e-02 2.50e+03 5.39e+01 bond pdb=" C25 UK1 R 501 " pdb=" N24 UK1 R 501 " ideal model delta sigma weight residual 1.384 1.516 -0.132 2.00e-02 2.50e+03 4.39e+01 ... (remaining 10374 not shown) Histogram of bond angle deviations from ideal: 70.00 - 83.47: 1 83.47 - 96.94: 0 96.94 - 110.41: 2475 110.41 - 123.87: 11019 123.87 - 137.34: 591 Bond angle restraints: 14086 Sorted by residual: angle pdb=" C21 UK1 R 501 " pdb=" C23 UK1 R 501 " pdb=" C27 UK1 R 501 " ideal model delta sigma weight residual 62.25 125.89 -63.64 3.00e+00 1.11e-01 4.50e+02 angle pdb=" C28 UK1 R 501 " pdb=" C57 UK1 R 501 " pdb=" C58 UK1 R 501 " ideal model delta sigma weight residual 109.49 70.00 39.49 3.00e+00 1.11e-01 1.73e+02 angle pdb=" N PRO A 115 " pdb=" CA PRO A 115 " pdb=" C PRO A 115 " ideal model delta sigma weight residual 110.70 99.23 11.47 1.22e+00 6.72e-01 8.83e+01 angle pdb=" C PHE A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta sigma weight residual 119.66 125.30 -5.64 7.30e-01 1.88e+00 5.96e+01 angle pdb=" N ASN A 14 " pdb=" CA ASN A 14 " pdb=" C ASN A 14 " ideal model delta sigma weight residual 113.41 105.34 8.07 1.22e+00 6.72e-01 4.37e+01 ... (remaining 14081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.04: 5685 20.04 - 40.07: 389 40.07 - 60.11: 46 60.11 - 80.15: 21 80.15 - 100.18: 6 Dihedral angle restraints: 6147 sinusoidal: 2462 harmonic: 3685 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C ASN A 371 " pdb=" N ASN A 371 " pdb=" CA ASN A 371 " pdb=" CB ASN A 371 " ideal model delta harmonic sigma weight residual -122.60 -135.35 12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C ARG A 317 " pdb=" N ARG A 317 " pdb=" CA ARG A 317 " pdb=" CB ARG A 317 " ideal model delta harmonic sigma weight residual -122.60 -110.51 -12.09 0 2.50e+00 1.60e-01 2.34e+01 ... (remaining 6144 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1275 0.090 - 0.179: 200 0.179 - 0.269: 45 0.269 - 0.358: 17 0.358 - 0.448: 5 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CA ASP R 293 " pdb=" N ASP R 293 " pdb=" C ASP R 293 " pdb=" CB ASP R 293 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C28 UK1 R 501 " pdb=" C57 UK1 R 501 " pdb=" C60 UK1 R 501 " pdb=" N24 UK1 R 501 " both_signs ideal model delta sigma weight residual False -2.64 -2.20 -0.44 2.00e-01 2.50e+01 4.78e+00 chirality pdb=" CA ASN A 371 " pdb=" N ASN A 371 " pdb=" C ASN A 371 " pdb=" CB ASN A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.16e+00 ... (remaining 1539 not shown) Planarity restraints: 1793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 290 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.71e+00 pdb=" C LEU R 290 " 0.045 2.00e-02 2.50e+03 pdb=" O LEU R 290 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR R 291 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 101 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C TYR R 101 " 0.045 2.00e-02 2.50e+03 pdb=" O TYR R 101 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG R 102 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 155 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C GLU A 155 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU A 155 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP A 156 " -0.015 2.00e-02 2.50e+03 ... (remaining 1790 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 303 2.69 - 3.24: 10570 3.24 - 3.79: 16952 3.79 - 4.35: 24311 4.35 - 4.90: 37159 Nonbonded interactions: 89295 Sorted by model distance: nonbonded pdb=" OH TYR B 105 " pdb=" O HOH B 401 " model vdw 2.134 2.440 nonbonded pdb=" OD1 ASP A 141 " pdb=" CD PRO A 143 " model vdw 2.158 3.440 nonbonded pdb=" OE1 GLU A 392 " pdb=" O HOH A 401 " model vdw 2.185 2.440 nonbonded pdb=" OE2 GLU A 209 " pdb=" O HOH A 402 " model vdw 2.244 2.440 nonbonded pdb=" N GLU A 145 " pdb=" OE1 GLU A 145 " model vdw 2.269 2.520 ... (remaining 89290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 5.960 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.200 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.244 10379 Z= 0.630 Angle : 1.295 63.641 14086 Z= 0.793 Chirality : 0.079 0.448 1542 Planarity : 0.005 0.047 1793 Dihedral : 14.299 100.185 3743 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.66 % Favored : 97.26 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.22), residues: 1240 helix: -1.26 (0.20), residues: 519 sheet: -0.58 (0.31), residues: 241 loop : -0.83 (0.28), residues: 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 179 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 187 average time/residue: 1.5894 time to fit residues: 314.6524 Evaluate side-chains 123 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 1.088 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.5019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 51 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS B 44 GLN B 88 ASN B 176 GLN B 268 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN N 31 ASN R 45 GLN R 99 HIS R 140 GLN R 338 ASN R 407 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 10379 Z= 0.189 Angle : 0.747 38.941 14086 Z= 0.352 Chirality : 0.042 0.245 1542 Planarity : 0.005 0.044 1793 Dihedral : 6.416 93.158 1390 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.23), residues: 1240 helix: 0.24 (0.21), residues: 524 sheet: -0.20 (0.32), residues: 246 loop : -0.25 (0.29), residues: 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 132 average time/residue: 1.6190 time to fit residues: 226.5097 Evaluate side-chains 117 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0881 time to fit residues: 1.7706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 176 GLN B 268 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10379 Z= 0.272 Angle : 0.764 37.976 14086 Z= 0.360 Chirality : 0.044 0.147 1542 Planarity : 0.005 0.048 1793 Dihedral : 6.606 97.547 1390 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.23), residues: 1240 helix: 0.66 (0.22), residues: 525 sheet: -0.04 (0.31), residues: 255 loop : -0.06 (0.30), residues: 460 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 117 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 15 residues processed: 137 average time/residue: 1.5908 time to fit residues: 230.9509 Evaluate side-chains 128 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 0.7336 time to fit residues: 5.6828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.3980 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10379 Z= 0.176 Angle : 0.698 37.706 14086 Z= 0.320 Chirality : 0.041 0.165 1542 Planarity : 0.004 0.051 1793 Dihedral : 6.287 94.243 1390 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1240 helix: 1.06 (0.22), residues: 528 sheet: 0.11 (0.32), residues: 255 loop : 0.02 (0.30), residues: 457 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 130 average time/residue: 1.7301 time to fit residues: 237.8605 Evaluate side-chains 121 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.227 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.1459 time to fit residues: 1.8946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 10379 Z= 0.190 Angle : 0.704 37.402 14086 Z= 0.322 Chirality : 0.042 0.157 1542 Planarity : 0.004 0.053 1793 Dihedral : 6.293 96.078 1390 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1240 helix: 1.23 (0.22), residues: 529 sheet: 0.35 (0.33), residues: 228 loop : 0.06 (0.29), residues: 483 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 109 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 129 average time/residue: 1.7052 time to fit residues: 232.7995 Evaluate side-chains 123 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 107 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.1180 time to fit residues: 2.0795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 98 optimal weight: 0.0050 chunk 55 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 88 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 10379 Z= 0.158 Angle : 0.679 37.489 14086 Z= 0.308 Chirality : 0.041 0.168 1542 Planarity : 0.004 0.052 1793 Dihedral : 6.140 95.005 1390 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer Outliers : 2.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1240 helix: 1.37 (0.22), residues: 529 sheet: 0.32 (0.33), residues: 228 loop : 0.09 (0.29), residues: 483 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 126 average time/residue: 1.7188 time to fit residues: 229.2191 Evaluate side-chains 120 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 1.181 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 1 average time/residue: 0.1622 time to fit residues: 1.8673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 0.0670 chunk 118 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.0000 overall best weight: 0.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 10379 Z= 0.139 Angle : 0.665 37.504 14086 Z= 0.298 Chirality : 0.040 0.176 1542 Planarity : 0.004 0.052 1793 Dihedral : 5.967 94.871 1390 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1240 helix: 1.55 (0.23), residues: 526 sheet: 0.42 (0.33), residues: 227 loop : 0.19 (0.29), residues: 487 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 135 average time/residue: 1.6408 time to fit residues: 235.2654 Evaluate side-chains 122 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1271 time to fit residues: 2.0624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 75 optimal weight: 0.4980 chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 0.0970 chunk 113 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 44 GLN B 268 ASN G 59 ASN N 1 GLN R 47 GLN R 407 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 10379 Z= 0.146 Angle : 0.681 37.339 14086 Z= 0.303 Chirality : 0.040 0.172 1542 Planarity : 0.004 0.052 1793 Dihedral : 5.986 95.815 1390 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1240 helix: 1.54 (0.23), residues: 531 sheet: 0.33 (0.33), residues: 238 loop : 0.24 (0.30), residues: 471 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 123 average time/residue: 1.7370 time to fit residues: 226.1325 Evaluate side-chains 121 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1425 time to fit residues: 1.8880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 116 optimal weight: 0.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10379 Z= 0.187 Angle : 0.705 37.099 14086 Z= 0.319 Chirality : 0.041 0.148 1542 Planarity : 0.004 0.052 1793 Dihedral : 6.165 96.991 1390 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1240 helix: 1.52 (0.23), residues: 522 sheet: 0.31 (0.33), residues: 239 loop : 0.31 (0.30), residues: 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 1.6893 time to fit residues: 221.7767 Evaluate side-chains 122 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1397 time to fit residues: 1.9055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 ASN B 16 ASN B 268 ASN G 59 ASN N 1 GLN R 47 GLN R 407 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10379 Z= 0.179 Angle : 0.705 37.218 14086 Z= 0.318 Chirality : 0.041 0.158 1542 Planarity : 0.004 0.052 1793 Dihedral : 6.140 96.238 1390 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.24), residues: 1240 helix: 1.49 (0.23), residues: 519 sheet: 0.34 (0.33), residues: 239 loop : 0.31 (0.29), residues: 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2480 Ramachandran restraints generated. 1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 14 residues processed: 123 average time/residue: 1.7199 time to fit residues: 223.8869 Evaluate side-chains 121 residues out of total 1095 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 1.308 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.9394 time to fit residues: 3.6279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 20.0000 chunk 14 optimal weight: 30.0000 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 59 GLN B 16 ASN B 268 ASN G 59 ASN N 1 GLN R 407 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.168116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102628 restraints weight = 11795.894| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.10 r_work: 0.3143 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10379 Z= 0.185 Angle : 0.704 37.159 14086 Z= 0.318 Chirality : 0.041 0.153 1542 Planarity : 0.004 0.051 1793 Dihedral : 6.167 96.961 1390 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1240 helix: 1.52 (0.23), residues: 518 sheet: 0.41 (0.33), residues: 237 loop : 0.34 (0.29), residues: 485 =============================================================================== Job complete usr+sys time: 4786.75 seconds wall clock time: 85 minutes 27.73 seconds (5127.73 seconds total)